Next Generation Sequencing Bioinformatics

Next generation sequencing has become an essential tool in genetic and
genomic analysis. It is increasingly important for experimental
scientists to gain the bioinformatics skills required to assess and
analyse the large volumes of sequencing data produced by next generation
sequencers. This next generation sequencing bioinformatics course aims to
equip participants with the essential informatics skills and knowledge
required to begin analysing next generation sequencing data and carry out
some of the most common types of analysis.

The programme will cover the algorithmic theory and principles of
bioinformatics, with a strong focus on practical computational sessions
using sequence analysis techniques and tools applicable to any species or
genome size. Accompanying the lecture and practical sessions will be a
series of seminars by invited speakers, who will highlight their
ground-breaking work in applications of next generation sequencing.

Please note: The practical sessions will be taught
exclusively through Unix/Linux. Therefore, participants are required to
have some previous exposure of using the Linux operating system. This
will be essential for participants to fully benefit from the course. The
course aims to provide a hands-on introduction to bioinformatics for next
generation sequencing, and should not be considered a complete education
in the theoretical and mathematical foundations of the topics.

Learning Outcomes
On completion of the course, participants can expect to have:

• A working knowledge of the unix command-line and writing basic shell scripts for automating bioinformatics tasks
• Knowledge of how to do QC assessment of high throughput sequencing data
• Understanding of the algorithmic concepts behind short read alignment and variant calling, and practical experience using the software
• Experience analysing RNA-Seq and CHiP-seq data for measuring abundance
• Knowledge of the organisation and sequencing data types available in public sequencing repositories

Please note: This course is aimed at applicants solely
interested in analysis of NGS data. Applicants interested in practical,
laboratory-based training in NGS technologies and methodologies should
consider our Next Generation Sequencing lab course. Details of
the 2016 lab course can be found here and is next scheduled for March
2017. Email
us for updates.

Feedback from the 2015 Next Generation Sequencing Bioinformatics
course

-Thank you for putting on such a wonderful course! I had a fantastic
time and recommend this course to all of my colleagues. I appreciated how
kind and patient all of the instructors were in teaching us what must be
second nature to them, particularly when it comes to using command line.
Thank you again!
-Greatly appreciate the effort done by all the course team; organizers,
instructors and WGC advanced courses staff members. All are professional,
helpful and dedicated to do the best. Thank you!
-The organizers and instructors were brilliant, incredibly patient and
generous with their time.
-Thank you so much for a wonderful week! So excited to get our data back
and be ready to jump into the analysis!
-I would just like to personally thank Thomas and Jacqui Keane for all
their hard work organising such a wonderful course. I learnt so much,
really enjoyed myself, made some great contacts and am now excited to put
my NGS bioinformatics skills to use. In addition, I’d like to thank all
the module leaders for their hard work and for delivering such excellent
modules. Finally, please pass on my thanks to those that are not named
module leaders but were the helpers (PhD students, bioinformaticians,
Postdocs etc) who were around during the practical sessions – they were
so patient and helpful answering my (almost) constant questions – thank
you so much!

The hands-on programme will cover several aspects of next generation
sequencing data analysis, including lectures, discussions and practical
computational sessions covering the following:

• Introduction to NGS technologies and tour of Sanger Institute facilities
• Introduction to the unix command line
• Introduction to scripting for bioinformatics
• NGS data formats and tools
• Sequence alignment+QC
• SNP/indel theory and practical
• Structural variation theory and practical
• De novo sequence assembly
• RNA-seq analysis
• ChiP-seq analysis
• Sequencing data visualisation with the Integrated Genomics Viewer
• Accessing public sequencing repositories
• Participant projects and presentations (final day)

Learning Outcomes
On completion of the course, participants can expect to have:

• A working knowledge of the unix command-line and writing basic shell scripts for automating bioinformatics tasks
• Knowledge of how to do QC assessment of high throughput sequencing data
• Understanding
  of the algorithmic concepts behind short read alignment and variant
  calling, and practical experience using the software
• Experience analysing RNA-Seq and CHiP-seq data for measuring abundance
• Knowledge of the organisation and sequencing data types available in public sequencing repositories

Course instructors
Thomas Keane Wellcome Trust Sanger Institute, UK
Jacqui Keane Wellcome Trust Sanger Institute, UK

Guest speakers
Mary O’Connell University of Leeds, UK
Clare Smith University of Massachusetts Medical School, USA
Aylwyn Scally University of Cambridge, UK
Stephen Bentley Wellcome Trust Sanger Institute, UK

Target audience and prerequisites
Applicants should be postdoctoral scientists, senior PhD students, junior
faculty members or clinicians actively engaged in or soon to commence
research involving next generation sequencing data analysis.

Linux experience: The practical sessions will
be taught
exclusively through Unix/Linux. Therefore, participants are
required to
have some previous exposure of using the Linux operating
system. This
will be essential for participants to fully benefit from
the course.

Cost
The
course is subsidised by the Wellcome Genome Campus Advanced Courses
and Scientific Conferences Programme. This is a residential
course and
there is a fee of £665 towards board and lodging for non-commercial
applicants. Please contact us for the commercial fee.

Applications
Applications for this course can be completed online. If you have any
problems with the online application process, please contact us.

Please note: Applications
must be supported by a
recommendation from a scientific or clinical sponsor (e.g. supervisor or
head of department). A request for a supporting
statement will be sent
to your nominated sponsor automatically during
the application process.
Applicants must ensure that their sponsor
provides this supporting
statement by the application deadline. Applications without a supporting
statement cannot be considered.

Deadlines
Deadline for Applications: Closed

Bursaries
Advanced Courses are subsidised for non-commercial
applicants from anywhere in the world. Additional, limited bursaries are
available (up to 50% of the course fee) and are awarded on merit. If you
would like to apply for a
bursary, please complete the bursary section
of the online application
form.

Please note that both the applicant
and sponsor are required to provide
a justification for the
bursary as part of the application.

Bursary terms and conditions

UK Courses (held at the Wellcome Genome Campus, Hinxton,
Cambridge)
A
limited number of bursaries are available for each course. These are
awarded by the selection committee according to merit. The bursary
covers a maximum of 50% of the course fee, though in exceptional
circumstances an application for the total course fee may be considered.
Where there are many bursary applications, the selection committee may
issue smaller amounts. We cannot assist with travel costs to attend UK
courses.

Overseas Courses (held outside of the UK)
A
limited number of bursaries are available for each course. These are
awarded on merit to cover travel, accommodation and sustenance. The
maximum award for travel (economy class) will be £750.

Bursaries can be applied for as part of the course application form.
Applicants
will be notified of a bursary award along with their place on
the
course, usually within one month of the application deadline. The
decision of the selection committee is
final.